1.) Clown_BD to extract, MKVMerge to create mkv
2.) Usually I bitstream from my Dune Smart H1 to an Anthem MRX-300.
3.) I have no idea, I don't even own a BD Player. I rip everything and play it that way. Actually, I do have a PS3, but I have not played Monsters University on it. I'll try it tonight and see. Scratch that, my PS3 is an old one and it does not have the option to bitstream HD audio. I have to decode it within the PS3 and send it out as PCM. I'll still try it, but it won't necessarily tell us anything. One other thing I didn't try was to let my Dune Smart decode the THD track and see if I got dropouts that way. I'll try that as well.
All in all, the only disks I have any issues with are Monsters University and The Walking Dead Season 1. Both disks have TrueHD 7.1 sound tracks, so...